PHI-base- The Pathogen Host database: Difference between revisions

From Planteome.org
Jump to navigation Jump to search
No edit summary
No edit summary
Line 1: Line 1:
Summary Correspondence by email: Alistair Irvine to Ramona Walls:
Summary Correspondence by email: Alistair Irvine to Ramona Walls:
Dr. Alistair Irvine, Postdoctoral Research Scientist, Rothamsted Research, Harpenden


* Pathogen-Host Interaction Database (PHI-base, http://www.phi-base.org/) which annotates pathogen genes based on known interactions with host organisms.   
* Pathogen-Host Interaction Database (PHI-base, http://www.phi-base.org/) which annotates pathogen genes based on known interactions with host organisms.   
* More information: Nucleic Acids Research http://nar.oxfordjournals.org/content/43/D1/D645.full.pdf.
* More information: Nucleic Acids Research http://nar.oxfordjournals.org/content/43/D1/D645.full.pdf.
 
* Interested in using ontologies to describing diseases in their database: Walls, R., et al. (2012). A plant disease extension of the Infectious Disease Ontology. International Conference on Biomedical Ontology 2012. Graz, Austria. 897: 1-5.
Obviously, one of the key aspects of any host-pathogen interaction is the disease that results from infection. I was hoping that the Plant Disease Ontology that you have been developing may be useful for describing diseases in our database. I read your interesting article from the 2012 Biomedical Ontology conference:
* Currently, curation of diseases in PHI-base is performed through a simple free text field. This causes predicable problems, as can be since from the list of unique disease names that I extracted from  our database and have attached to this email.
Walls, R., et al. (2012). A plant disease extension of the Infectious Disease Ontology. International Conference on Biomedical Ontology 2012. Graz, Austria. 897: 1-5.
 
Currently, curation of diseases in PHI-base is performed through a simple free text field. This causes predicable problems, as can be since from the list of unique disease names that I extracted from  our database and have attached to this email.


In your 2012 paper, you mention that researchers should contact you before using IDOPlant, because it was still under development. I wish to enquire about the current status of this project and if the plant disease terms would be sufficient to describe the diseases in our database (attached).
In your 2012 paper, you mention that researchers should contact you before using IDOPlant, because it was still under development. I wish to enquire about the current status of this project and if the plant disease terms would be sufficient to describe the diseases in our database (attached).


I have downloaded the latest available Plant Disease Ontology OBO file from http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/collaborators_ontology/plant_disease/plant_disease_ontology.obo?view=log, but when I attempted to find diseases from our database I was not successful.
* Downloaded the latest available Plant Disease Ontology OBO file from http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/collaborators_ontology/plant_disease/plant_disease_ontology.obo?view=log, but when I attempted to find diseases from our database I was not successful.


In addition to the disease, we do capture data regarding pathogen species, host species, infected tissue, inducers, anti-infective agent and more. Given the methodology in your paper, we could use this information to define the disease.
In addition to the disease, we do capture data regarding pathogen species, host species, infected tissue, inducers, anti-infective agent and more. Given the methodology in your paper, we could use this information to define the disease.
I would appreciate any advice you may be able to give regarding how we may be able to use your ontology to describe diseases in PHI-base.
Kind Regards,
Dr. Alistair Irvine, Postdoctoral Research Scientist, Rothamsted Research, Harpenden
http://www.phi-base.org/

Revision as of 01:35, 1 April 2015

Summary Correspondence by email: Alistair Irvine to Ramona Walls: Dr. Alistair Irvine, Postdoctoral Research Scientist, Rothamsted Research, Harpenden

  • Pathogen-Host Interaction Database (PHI-base, http://www.phi-base.org/) which annotates pathogen genes based on known interactions with host organisms.
  • More information: Nucleic Acids Research http://nar.oxfordjournals.org/content/43/D1/D645.full.pdf.
  • Interested in using ontologies to describing diseases in their database: Walls, R., et al. (2012). A plant disease extension of the Infectious Disease Ontology. International Conference on Biomedical Ontology 2012. Graz, Austria. 897: 1-5.
  • Currently, curation of diseases in PHI-base is performed through a simple free text field. This causes predicable problems, as can be since from the list of unique disease names that I extracted from our database and have attached to this email.

In your 2012 paper, you mention that researchers should contact you before using IDOPlant, because it was still under development. I wish to enquire about the current status of this project and if the plant disease terms would be sufficient to describe the diseases in our database (attached).

In addition to the disease, we do capture data regarding pathogen species, host species, infected tissue, inducers, anti-infective agent and more. Given the methodology in your paper, we could use this information to define the disease.

Retrieved from "https://wiki.planteome.org/index.php?title=PHI-base-_The_Pathogen_Host_database&oldid=796"